PROJECT SUMMARY Although great efforts have been dedicated to characterizing neuronal cell types in the brain, systematic studies on the brain-spinal cord connectome and associated spinal neuronal types are lacking. In this project, a team of seven laboratories proposes to use a highly innovative and multidisciplinary approach to systematically characterize neuronal types in the spinal cord based on their anatomy, connectivity, neuronal morphologies, molecular identities, and electrophysiological properties. In Aim 1, we will use a newly developed AAV anterograde transsynaptic tagging method to label spinal cord neurons that receive descending inputs from different brain regions, and use a retrograde viral tracer, AAVretro, to label spinal neurons that project to defined brain regions. These tagged neurons will be imaged in the intact whole spinal cord with a newly developed fast 3D light sheet microscopy technique, and targeted for recording in slice preparations. The axonal collateral patterns, dendritic morphologies, and electrophysiological properties will be compared between different input/output-defined spinal neuron groups. In Aim 2, the gene expression patterns of the tagged neurons will be determined in situ by sequential bar-coded FISH (seqFISH), with candidate marker genes obtained from online resources, or from single-cell sorting and RNA sequencing (Dropseq). In Aim 3, all collected data on connectivity, anatomical cell type distribution map, neuronal morphologies, molecular identities, and electrophysiological properties will be used for classifying spinal neuron types connected with brain, and an open-source data portal will be established which will allow users to search, view, and analyze the multi-modal and integrative cell-type specific data. Together, we aim to construct a comprehensive cell- type atlas of the mouse brain-spinal cord connectome.